I think it is a mistake to assume that homophobia has its origins in religion. I think religion is used by the homophobic to justify and feed their own fears, but the phobia isn't against the gays and lesbians out in the world, it is internal.

It has been my experience as a gay man that many, if not most, homophobic people are actually battling themselves and their homosexual desires. Our culture has so demonized gays (much less so lesbians, since straight men like watching two women getting it on... which is why lesbian porn is found on straight porn sites) that gay men remain closeted and take a position of homophobia to conceal their true desires.

I think the point of masculinity is also a good one, but i think most people would be surprised to learn how many masculine gays there are out there. Check sites for "Bears" and leather fetishes. These are masculine, rough, motorcycle gang type guys that hardly fit the typical queen stereo-type. And these are just the extreme. There are many masculine gays, myself included, that go about their day getting hit on by straight women and largely ignored by gay men.

While religion has a great influence on a person's view of marriage and what is right and wrong, I think whether homosexuality is wrong is something everyone decides personally.
I am an atheist but do not agree with homosexuality at all. However, that doesn't mean I am against equal rights. Like a few people have mentioned, same-gender attraction just doesn't match with natural femininity and masculinity, and straight relationships are obviously the most natural of unions, but that doesn't mean homosexuals can be denied to marry or be discriminated against.

As others have said, being an atheist does not automatically make you a better person. There are evil, asshole, and nasty atheists as well. People are bad. Period. However, I would like to think that if polled, the atheist community is measurably more accepting and tolerance of the LGBT community and all others regardless of gender, race, sexual preference etc...